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TreeFam - database of animal gene trees

(Release 9, March 2013, 109 species, 15,736 families)

TreeFam is a database composed of phylogenetic trees inferred from animal genomes. It provides orthology/parology predictions as well the evolutionary history of genes.
(see the BRCA2 gene family page as an example).

Search TreeFam

(HMM-based protein sequence search vs. TreeFam & Pfam HMMs)
Insert into tree
Insert into TreeFam gene tree using

Parsimony (citing_treefamsuper-fast, citing_treefammight insert into several branches)
Maximum Likelihood (citing_treefammore accurate, citing_treefammight take a bit longer)

Species in TreeFam

Species Tree used in TreeFam 9. See full tree here.

The TreeFam project

citing_treefam TreeFam news

  • citing_treefam Feature: TreeFam family visualisation available: [...]
    (posted 19 Feb 2014)
  • citing_treefam Feature: Tree Insertion available: [...]
    (posted 9 Sept 2013)
  • citing_treefam Suggestion: Downloading the full gene tree view: [...]
    (posted 3 May 2013)
  • citing_treefam Suggestion: Domain diagrams as hyperlinks to Pfam: [...]
    (posted 3 May 2013)
  • citing_treefam TreeFam 9 is now available: [...]
    (posted 3 May 2013)
  • citing_treefam TreeFam: What is in the next release: [...]
    (posted 10 December 2012)
  • citing_treefam We are on the move: [...]
    (posted 1 November 2012)
  • citing_treefam TreeFam is back with a new release: [...]
    (posted 27 March 2012)

citing_treefam Why our data is good

Learn about how TreeFam builds families, alignments, and trees and how families defined in TreeFam.


citing_treefam Link to TreeFam data

TreeFam families
There are many ways you can link to TreeFam data. Learn how you can link to e.g. our gene families.

Gene tree widget
You can add our gene tree widget to your website: e.g. simply point an iframe to our trees using a TreeFam family ID or a sequence identifier.


citing_treefam Xfam databases

Protein domains:
RNA families:
Repetitive DNA:
Peptidases:
Spurious ORFs:

citing_treefam Using TreeFam

Data download
Download all our data: e.g. alignments, hmms, trees, pairwise orthologs, external references and more.

API
Programmatically fetch data through our API and see a list of example scripts in our github repository. Use treefamscan to score your sequences against TreeFam hmms.

Citing
If you find TreeFam useful, please consider citing the references that describe this work:
TreeFam: 2008 Update Jue Ruan, Heng Li, et al. Nucleic Acids Research (2008)
doi: 10.1093/nar/gkm1005